Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

PI(4,5)P2: signaling the plasma membrane

RC Wills, GRV Hammond - Biochemical Journal, 2022 - portlandpress.com
In the almost 70 years since the first hints of its existence, the phosphoinositide,
phosphatidyl-D-myo-inositol 4, 5-bisphosphate has been found to be central in the …

Allosteric activation of T cell antigen receptor signaling by quaternary structure relaxation

AL Lanz, G Masi, N Porciello, A Cohnen, D Cipria… - Cell reports, 2021 - cell.com
The mechanism of T cell antigen receptor (TCR-CD3) signaling remains elusive. Here, we
identify mutations in the transmembrane region of TCRβ or CD3ζ that augment peptide …

A novel homeostatic mechanism tunes PI (4, 5) P2-dependent signaling at the plasma membrane

RC Wills, CP Doyle, JP Zewe, J Pacheco… - Journal of Cell …, 2023 - journals.biologists.com
ABSTRACT The lipid molecule phosphatidylinositol (4, 5)-bisphosphate [PI (4, 5) P 2]
controls all aspects of plasma membrane (PM) function in animal cells, from its selective …

A brief history of visualizing membrane systems in molecular dynamics simulations

RA Corey, M Baaden, M Chavent - Frontiers in Bioinformatics, 2023 - frontiersin.org
Understanding lipid dynamics and function, from the level of single, isolated molecules to
large assemblies, is more than ever an intensive area of research. The interactions of lipids …

Assessing the martini 3 protein model: A review of its path and potential

L Borges-Araújo, GP Pereira, M Valério… - Biochimica et Biophysica …, 2024 - Elsevier
Coarse-grained (CG) protein models have become indispensable tools for studying many
biological protein details, from conformational dynamics to the organization of protein macro …

Membrane Heteroreceptor Complexes as Second-Order Protein Modulators: A Novel Integrative Mechanism through Allosteric Receptor–Receptor Interactions

M Mirchandani-Duque, M Choucri… - Membranes, 2024 - mdpi.com
Bioluminescence and fluorescence resonance energy transfer (BRET and FRET) together
with the proximity ligation method revealed the existence of G-protein-coupled receptors …

Probing the energy landscape of the lipid interactions of the Serotonin1A receptor

M Mohole, A Naglekar, D Sengupta… - Biophysical …, 2024 - Elsevier
G protein-coupled receptors (GPCRs) are lipid-regulated transmembrane proteins that play
a central role in cell signaling and pharmacology. Although the role of membrane lipids in …

[HTML][HTML] Simulation-predicted and-explained inheritance model of pathogenicity confirmed by transgenic mice models

CY Tsai, YC Lu, YH Chan, N Radhakrishnan… - Computational and …, 2023 - Elsevier
Variants in the gap junction beta-2 (GJB2) gene are the most common cause of hereditary
hearing impairment. However, how GJB2 variants lead to local physicochemical and …

Cardiolipin occupancy profiles of YidC paralogs reveal the significance of respective TM2 helix residues in determining paralog-specific phenotypes

S Mishra, EJ van Aalst, BJ Wylie… - Frontiers in Molecular …, 2023 - frontiersin.org
YidC belongs to an evolutionarily conserved family of insertases, YidC/Oxa1/Alb3, in
bacteria, mitochondria, and chloroplasts, respectively. Unlike Gram-negative bacteria, Gram …